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Sub-GOFA: A tool for Sub-Gene Ontology function analysis in clonal mosaicism using semantic (logical) similarity



Tadaaki Katsuda1,*, Noriko Sato1, Kaoru Mogushi2,3, Takeshi Hase2,3,4,5 & Masaaki Muramatsu1



1Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 24F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan; 2Institute of Education, Tokyo Medical and Dental University, 20F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan; 3Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan; 4The Systems Biology Institute, SaiseiIkedayama Bldg. 5-10-25 Higashi Gotanda Shinagawa, Tokyo, 141-0022, Japan; 5SBX BioSciences, Inc, 1600 - 925 West Georgia Street, Vancouver, BC V6C 3L2, Canada; *Corresponding author



Tadaaki Katsuda - tadakatsuda.epi@mri.tmd.ac.jp; Noriko Sato - nsato.epi@mri.tmd.ac.jp; Kaoru Mogushi - mogushi.mds@tmd.ac.jp; Takeshi Hase - 2121adm@tmd.ac.jp; Masaaki Muramatsu - muramatsu.epi@mri.tmd.ac.jp


Article Type

Research Article



Received November 22, 2021; Revised December 10, 2021; Accepted December 16, 2021, Published January 31, 2022



Clonal mosaicism (a detectable post-zygotic mutational event in cellular subpopulations) is common in cancer patients. Detected segments of clonal mosaicism are usually bundled into large-locus regions for statistical analysis. However, low-frequency genes are overlooked and are not sufficient to elucidate qualitative differences between cancer patients and non-patients. Therefore, it is of interest to develop and describe a tool named Sub-GOFA for Sub-Gene Ontology function analysis in clonal mosaicism using semantic similarity. Sub-GOFA measures the semantic (logical) similarity among patients using the sub-GO network structures of various sizes segmented from the gene ontology (GO) for clustering analysis. The sub-GOs root-terms with significant differences are extracted as disease-associated genetic functions. Sub-GOFA selected a high ratio of cancer-associated genes under validation with acceptable threshold.



Sub-GOFA, tool, sub-gene ontology, function, clonal mosaicism, semantic, logical, similarity



Katsuda et al. Bioinformation 18(1): 53-60 (2022)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.